from __future__ import absolute_import, division, print_function from mmtbx.secondary_structure.build import ss_idealization as ssb import iotbx.pdb from libtbx.test_utils import approx_equal from scitbx.array_family import flex from six.moves import zip t_pdb_str = """\ ATOM 1 N ALA 2 1.643 -2.366 -1.408 1.00 ATOM 3 CA ALA 2 1.280 -3.608 -2.069 1.00 ATOM 6 CB ALA 2 1.361 -4.762 -1.068 1.00 ATOM 10 C ALA 2 -0.114 -3.466 -2.684 1.00 ATOM 11 O ALA 2 -0.327 -3.827 -3.840 1.00 """ alpha_pdb_str = """\ ATOM 1 N ALA 2 1.643 -2.366 -1.408 1.00 ATOM 3 CA ALA 2 1.280 -3.608 -2.069 1.00 ATOM 6 CB ALA 2 1.361 -4.762 -1.068 1.00 ATOM 10 C ALA 2 -0.114 -3.466 -2.684 1.00 ATOM 11 O ALA 2 -0.327 -3.827 -3.840 1.00 ATOM 12 N ALA 3 -1.028 -2.938 -1.882 1.00 ATOM 14 CA ALA 3 -2.395 -2.743 -2.333 1.00 ATOM 17 CB ALA 3 -3.228 -2.150 -1.194 1.00 ATOM 21 C ALA 3 -2.396 -1.855 -3.579 1.00 ATOM 22 O ALA 3 -3.059 -2.167 -4.567 1.00 """ correct_answer = """\ ATOM 1 N ALA A 1 1.643 -2.366 -1.408 1.00 0.00 ATOM 2 CA ALA A 1 1.280 -3.608 -2.069 1.00 0.00 ATOM 3 C ALA A 1 -0.114 -3.466 -2.684 1.00 0.00 ATOM 4 O ALA A 1 -0.327 -3.827 -3.840 1.00 0.00 ATOM 5 CB ALA A 1 1.308 -4.763 -1.090 1.00 0.00 C ATOM 6 N CYS A 2 -1.028 -2.938 -1.882 1.00 0.00 ATOM 7 CA CYS A 2 -2.395 -2.743 -2.332 1.00 0.00 ATOM 8 C CYS A 2 -2.396 -1.855 -3.579 1.00 0.00 ATOM 9 O CYS A 2 -3.059 -2.167 -4.567 1.00 0.00 ATOM 10 CB CYS A 2 -3.238 -2.101 -1.237 1.00 0.00 C ATOM 11 SG CYS A 2 -3.482 -3.154 0.212 1.00 0.00 S ATOM 12 N GLU A 3 -1.646 -0.767 -3.491 1.00 0.00 ATOM 13 CA GLU A 3 -1.551 0.168 -4.599 1.00 0.00 ATOM 14 C GLU A 3 -1.044 -0.568 -5.841 1.00 0.00 ATOM 15 O GLU A 3 -1.601 -0.419 -6.927 1.00 0.00 ATOM 16 CB GLU A 3 -0.610 1.317 -4.257 1.00 0.00 C ATOM 17 CG GLU A 3 -1.140 2.237 -3.169 1.00 0.00 C ATOM 18 CD GLU A 3 -0.179 3.362 -2.837 1.00 0.00 C ATOM 19 OE1 GLU A 3 0.954 3.354 -3.365 1.00 0.00 O ATOM 20 OE2 GLU A 3 -0.554 4.255 -2.048 1.00 0.00 O ATOM 21 N ASP A 4 0.008 -1.348 -5.639 1.00 0.00 ATOM 22 CA ASP A 4 0.597 -2.109 -6.728 1.00 0.00 ATOM 23 C ASP A 4 -0.466 -3.023 -7.340 1.00 0.00 ATOM 24 O ASP A 4 -0.611 -3.085 -8.559 1.00 0.00 ATOM 25 CB ASP A 4 1.773 -2.941 -6.231 1.00 0.00 C ATOM 26 CG ASP A 4 2.495 -3.656 -7.355 1.00 0.00 C ATOM 27 OD1 ASP A 4 3.222 -2.985 -8.118 1.00 0.00 O ATOM 28 OD2 ASP A 4 2.337 -4.889 -7.477 1.00 0.00 O ATOM 29 N GLY A 5 -1.184 -3.711 -6.463 1.00 0.00 ATOM 30 CA GLY A 5 -2.231 -4.619 -6.901 1.00 0.00 ATOM 31 C GLY A 5 -3.253 -3.847 -7.737 1.00 0.00 ATOM 32 O GLY A 5 -3.647 -4.296 -8.813 1.00 0.00 ATOM 33 N PHE A 6 -3.654 -2.699 -7.211 1.00 0.00 ATOM 34 CA PHE A 6 -4.623 -1.860 -7.896 1.00 0.00 ATOM 35 C PHE A 6 -4.090 -1.499 -9.284 1.00 0.00 ATOM 36 O PHE A 6 -4.809 -1.602 -10.276 1.00 0.00 ATOM 37 CB PHE A 6 -4.896 -0.590 -7.098 1.00 0.00 C ATOM 38 CG PHE A 6 -5.613 -0.838 -5.803 1.00 0.00 C ATOM 39 CD1 PHE A 6 -6.985 -1.027 -5.781 1.00 0.00 C ATOM 40 CD2 PHE A 6 -4.916 -0.882 -4.606 1.00 0.00 C ATOM 41 CE1 PHE A 6 -7.649 -1.255 -4.589 1.00 0.00 C ATOM 42 CE2 PHE A 6 -5.574 -1.110 -3.411 1.00 0.00 C ATOM 43 CZ PHE A 6 -6.942 -1.297 -3.404 1.00 0.00 C ATOM 44 N ILE A 7 -2.831 -1.084 -9.309 1.00 0.00 ATOM 45 CA ILE A 7 -2.192 -0.708 -10.559 1.00 0.00 ATOM 46 C ILE A 7 -2.243 -1.890 -11.529 1.00 0.00 ATOM 47 O ILE A 7 -2.600 -1.727 -12.695 1.00 0.00 ATOM 48 CB ILE A 7 -0.732 -0.284 -10.349 1.00 0.00 C ATOM 49 CG1 ILE A 7 0.091 -1.437 -9.762 1.00 0.00 C ATOM 50 CG2 ILE A 7 -0.673 0.933 -9.437 1.00 0.00 C ATOM 51 CD1 ILE A 7 1.586 -1.180 -9.736 1.00 0.00 C ATOM 52 N HIS A 8 -1.881 -3.055 -11.012 1.00 0.00 ATOM 53 CA HIS A 8 -1.882 -4.264 -11.817 1.00 0.00 ATOM 54 C HIS A 8 -3.285 -4.496 -12.382 1.00 0.00 ATOM 55 O HIS A 8 -3.442 -4.772 -13.570 1.00 0.00 ATOM 56 CB HIS A 8 -1.451 -5.466 -10.986 1.00 0.00 C ATOM 57 CG HIS A 8 -0.031 -5.390 -10.518 1.00 0.00 C ATOM 58 ND1 HIS A 8 1.041 -5.612 -11.354 1.00 0.00 N ATOM 59 CD2 HIS A 8 0.493 -5.116 -9.299 1.00 0.00 C ATOM 60 CE1 HIS A 8 2.164 -5.479 -10.671 1.00 0.00 C ATOM 61 NE2 HIS A 8 1.859 -5.178 -9.422 1.00 0.00 N ATOM 62 N LYS A 9 -4.269 -4.376 -11.503 1.00 0.00 ATOM 63 CA LYS A 9 -5.653 -4.568 -11.898 1.00 0.00 ATOM 64 C LYS A 9 -6.000 -3.590 -13.022 1.00 0.00 ATOM 65 O LYS A 9 -6.590 -3.978 -14.029 1.00 0.00 ATOM 66 CB LYS A 9 -6.588 -4.352 -10.714 1.00 0.00 C ATOM 67 CG LYS A 9 -6.476 -5.423 -9.642 1.00 0.00 C ATOM 68 CD LYS A 9 -7.452 -5.175 -8.504 1.00 0.00 C ATOM 69 CE LYS A 9 -7.325 -6.235 -7.421 1.00 0.00 C ATOM 70 NZ LYS A 9 -8.267 -5.998 -6.293 1.00 0.00 N ATOM 71 N MET A 10 -5.617 -2.338 -12.812 1.00 0.00 ATOM 72 CA MET A 10 -5.879 -1.301 -13.795 1.00 0.00 ATOM 73 C MET A 10 -5.242 -1.695 -15.130 1.00 0.00 ATOM 74 O MET A 10 -5.880 -1.605 -16.177 1.00 0.00 ATOM 75 CB MET A 10 -5.315 0.036 -13.329 1.00 0.00 C ATOM 76 CG MET A 10 -6.072 0.644 -12.159 1.00 0.00 C ATOM 77 SD MET A 10 -5.738 -0.196 -10.599 1.00 0.00 S ATOM 78 CE MET A 10 -6.442 0.965 -9.431 1.00 0.00 C ATOM 79 N LEU A 11 -3.991 -2.124 -15.047 1.00 0.00 ATOM 80 CA LEU A 11 -3.261 -2.533 -16.235 1.00 0.00 ATOM 81 C LEU A 11 -4.024 -3.658 -16.937 1.00 0.00 ATOM 82 O LEU A 11 -4.213 -3.623 -18.151 1.00 0.00 ATOM 83 CB LEU A 11 -1.859 -3.009 -15.869 1.00 0.00 C ATOM 84 CG LEU A 11 -0.901 -1.945 -15.320 1.00 0.00 C ATOM 85 CD1 LEU A 11 0.404 -2.587 -14.875 1.00 0.00 C ATOM 86 CD2 LEU A 11 -0.638 -0.851 -16.346 1.00 0.00 C ATOM 87 N ASN A 12 -4.443 -4.631 -16.140 1.00 0.00 ATOM 88 CA ASN A 12 -5.183 -5.765 -16.669 1.00 0.00 ATOM 89 C ASN A 12 -6.440 -5.262 -17.382 1.00 0.00 ATOM 90 O ASN A 12 -6.738 -5.685 -18.497 1.00 0.00 ATOM 91 CB ASN A 12 -5.566 -6.727 -15.557 1.00 0.00 C ATOM 92 CG ASN A 12 -4.368 -7.481 -15.014 1.00 0.00 C ATOM 93 OD1 ASN A 12 -3.501 -7.919 -15.770 1.00 0.00 O ATOM 94 ND2 ASN A 12 -4.314 -7.637 -13.696 1.00 0.00 N ATOM 95 N GLN A 13 -7.144 -4.364 -16.707 1.00 0.00 ATOM 96 CA GLN A 13 -8.362 -3.798 -17.261 1.00 0.00 ATOM 97 C GLN A 13 -8.047 -3.133 -18.603 1.00 0.00 ATOM 98 O GLN A 13 -8.755 -3.341 -19.586 1.00 0.00 ATOM 99 CB GLN A 13 -8.966 -2.779 -16.302 1.00 0.00 C ATOM 100 CG GLN A 13 -10.288 -2.188 -16.771 1.00 0.00 C ATOM 101 CD GLN A 13 -10.889 -1.230 -15.763 1.00 0.00 C ATOM 102 OE1 GLN A 13 -10.303 -0.967 -14.712 1.00 0.00 O ATOM 103 NE2 GLN A 13 -12.066 -0.701 -16.077 1.00 0.00 N ATOM 104 N PRO A 14 -6.981 -2.345 -18.600 1.00 0.00 ATOM 105 CA PRO A 14 -6.562 -1.648 -19.804 1.00 0.00 ATOM 106 C PRO A 14 -6.302 -2.668 -20.915 1.00 0.00 ATOM 107 O PRO A 14 -6.758 -2.492 -22.043 1.00 0.00 ATOM 108 CB PRO A 14 -5.265 -0.968 -19.395 1.00 0.00 C ATOM 109 CG PRO A 14 -5.393 -0.780 -17.926 1.00 0.00 C ATOM 110 CD PRO A 14 -6.119 -1.992 -17.421 1.00 0.00 C ATOM 111 N SER A 15 -5.570 -3.712 -20.555 1.00 0.00 ATOM 112 CA SER A 15 -5.244 -4.761 -21.507 1.00 0.00 ATOM 113 C SER A 15 -6.538 -5.354 -22.070 1.00 0.00 ATOM 114 O SER A 15 -6.671 -5.527 -23.280 1.00 0.00 ATOM 115 CB SER A 15 -4.417 -5.855 -20.843 1.00 0.00 C ATOM 116 OG SER A 15 -4.136 -6.904 -21.753 1.00 0.00 O ATOM 117 N ARG A 16 -7.458 -5.648 -21.163 1.00 0.00 ATOM 118 CA ARG A 16 -8.737 -6.218 -21.553 1.00 0.00 ATOM 119 C ARG A 16 -9.432 -5.275 -22.538 1.00 0.00 ATOM 120 O ARG A 16 -9.931 -5.711 -23.574 1.00 0.00 ATOM 121 CB ARG A 16 -9.625 -6.440 -20.333 1.00 10.00 C ATOM 122 CG ARG A 16 -9.062 -7.437 -19.324 1.00 10.00 C ATOM 123 CD ARG A 16 -8.986 -8.857 -19.879 1.00 10.00 C ATOM 124 NE ARG A 16 -10.308 -9.411 -20.184 1.00 10.00 N ATOM 125 CZ ARG A 16 -10.555 -10.473 -20.955 1.00 10.00 C ATOM 126 NH1 ARG A 16 -9.582 -11.166 -21.548 1.00 10.00 N ATOM 127 NH2 ARG A 16 -11.812 -10.855 -21.138 1.00 10.00 N ATOM 128 N THR A 17 -9.442 -4.000 -22.179 1.00 0.00 ATOM 129 CA THR A 17 -10.067 -2.991 -23.017 1.00 0.00 ATOM 130 C THR A 17 -9.418 -3.011 -24.403 1.00 0.00 ATOM 131 O THR A 17 -10.112 -3.007 -25.418 1.00 0.00 ATOM 132 CB THR A 17 -9.922 -1.586 -22.421 1.00 0.00 C ATOM 133 OG1 THR A 17 -8.535 -1.249 -22.296 1.00 0.00 O ATOM 134 CG2 THR A 17 -10.584 -1.520 -21.053 1.00 0.00 C ATOM 135 N TRP A 18 -8.093 -3.034 -24.400 1.00 0.00 ATOM 136 CA TRP A 18 -7.342 -3.056 -25.643 1.00 0.00 ATOM 137 C TRP A 18 -7.761 -4.276 -26.467 1.00 0.00 ATOM 138 O TRP A 18 -8.021 -4.163 -27.663 1.00 0.00 ATOM 139 CB TRP A 18 -5.844 -3.104 -25.369 1.00 0.00 C ATOM 140 CG TRP A 18 -5.314 -1.843 -24.760 1.00 0.00 C ATOM 141 CD1 TRP A 18 -5.088 -1.602 -23.436 1.00 0.00 C ATOM 142 CD2 TRP A 18 -4.942 -0.645 -25.454 1.00 0.00 C ATOM 143 NE1 TRP A 18 -4.599 -0.330 -23.263 1.00 0.00 N ATOM 144 CE2 TRP A 18 -4.500 0.278 -24.486 1.00 0.00 C ATOM 145 CE3 TRP A 18 -4.941 -0.264 -26.800 1.00 0.00 C ATOM 146 CZ2 TRP A 18 -4.061 1.557 -24.820 1.00 0.00 C ATOM 147 CZ3 TRP A 18 -4.504 1.006 -27.130 1.00 0.00 C ATOM 148 CH2 TRP A 18 -4.070 1.902 -26.144 1.00 0.00 C ATOM 149 N VAL A 19 -7.813 -5.415 -25.792 1.00 0.00 ATOM 150 CA VAL A 19 -8.197 -6.655 -26.445 1.00 0.00 ATOM 151 C VAL A 19 -9.587 -6.493 -27.064 1.00 0.00 ATOM 152 O VAL A 19 -9.803 -6.858 -28.218 1.00 0.00 ATOM 153 CB VAL A 19 -8.224 -7.833 -25.460 1.00 0.00 C ATOM 154 CG1 VAL A 19 -8.745 -9.091 -26.144 1.00 0.00 C ATOM 155 CG2 VAL A 19 -6.836 -8.068 -24.880 1.00 0.00 C ATOM 156 N TYR A 20 -10.493 -5.943 -26.268 1.00 0.00 ATOM 157 CA TYR A 20 -11.856 -5.727 -26.723 1.00 0.00 ATOM 158 C TYR A 20 -11.839 -4.848 -27.975 1.00 0.00 ATOM 159 O TYR A 20 -12.504 -5.155 -28.963 1.00 0.00 ATOM 160 CB TYR A 20 -12.690 -5.063 -25.634 1.00 0.00 C ATOM 161 CG TYR A 20 -12.961 -5.962 -24.448 1.00 0.00 C ATOM 162 CD1 TYR A 20 -12.741 -7.332 -24.525 1.00 0.00 C ATOM 163 CD2 TYR A 20 -13.437 -5.441 -23.252 1.00 0.00 C ATOM 164 CE1 TYR A 20 -12.987 -8.157 -23.444 1.00 0.00 C ATOM 165 CE2 TYR A 20 -13.686 -6.259 -22.165 1.00 0.00 C ATOM 166 CZ TYR A 20 -13.459 -7.615 -22.267 1.00 0.00 C ATOM 167 OH TYR A 20 -13.705 -8.433 -21.187 1.00 0.00 O TER """ alpha_helix_template="""\ ATOM 1 N ALA 1 -1.204 -0.514 0.643 1.00 0.00 N ATOM 2 CA ALA 1 0.000 0.000 0.000 1.00 0.00 C ATOM 3 CB ALA 1 0.808 0.860 0.974 1.00 0.00 C ATOM 4 C ALA 1 0.866 -1.134 -0.537 1.00 0.00 C ATOM 5 O ALA 1 1.432 -1.035 -1.625 1.00 0.00 O ATOM 6 N ALA 2 0.965 -2.213 0.234 1.00 0.00 N ATOM 7 CA ALA 2 1.761 -3.368 -0.162 1.00 0.00 C ATOM 8 CB ALA 2 1.751 -4.434 0.936 1.00 0.00 C ATOM 9 C ALA 2 1.258 -3.963 -1.472 1.00 0.00 C ATOM 10 O ALA 2 2.047 -4.366 -2.327 1.00 0.00 O """ alpha_helix_answer="""\ ATOM 1 N ALA 1 -1.204 -0.514 0.643 1.00 0.00 N ATOM 2 CA ALA 1 0.000 0.000 0.000 1.00 0.00 C ATOM 3 CB ALA 1 0.808 0.860 0.974 1.00 0.00 C ATOM 4 C ALA 1 0.866 -1.134 -0.537 1.00 0.00 C ATOM 5 O ALA 1 1.432 -1.035 -1.625 1.00 0.00 O ATOM 6 N ALA 2 0.965 -2.213 0.234 1.00 0.00 N ATOM 7 CA ALA 2 1.761 -3.368 -0.162 1.00 0.00 C ATOM 8 CB ALA 2 1.751 -4.434 0.936 1.00 0.00 C ATOM 9 C ALA 2 1.258 -3.963 -1.472 1.00 0.00 C ATOM 10 O ALA 2 2.047 -4.366 -2.327 1.00 0.00 O ATOM 11 N ALA 3 -0.062 -4.016 -1.625 1.00 0.00 N ATOM 12 CA ALA 3 -0.673 -4.562 -2.830 1.00 0.00 C ATOM 13 CB ALA 3 -2.199 -4.560 -2.711 1.00 0.00 C ATOM 14 C ALA 3 -0.245 -3.782 -4.068 1.00 0.00 C ATOM 15 O ALA 3 0.011 -4.364 -5.123 1.00 0.00 O ATOM 16 N ALA 4 -0.168 -2.462 -3.934 1.00 0.00 N ATOM 17 CA ALA 4 0.229 -1.600 -5.040 1.00 0.00 C ATOM 18 CB ALA 4 0.169 -0.128 -4.627 1.00 0.00 C ATOM 19 C ALA 4 1.628 -1.946 -5.537 1.00 0.00 C ATOM 20 O ALA 4 1.888 -1.949 -6.740 1.00 0.00 O ATOM 21 N ALA 5 2.529 -2.239 -4.602 1.00 0.00 N ATOM 22 CA ALA 5 3.902 -2.587 -4.943 1.00 0.00 C ATOM 23 CB ALA 5 4.732 -2.811 -3.677 1.00 0.00 C ATOM 24 C ALA 5 3.954 -3.827 -5.827 1.00 0.00 C ATOM 25 O ALA 5 4.744 -3.899 -6.767 1.00 0.00 O ATOM 26 N ALA 6 3.104 -4.804 -5.520 1.00 0.00 N ATOM 27 CA ALA 6 3.052 -6.043 -6.286 1.00 0.00 C ATOM 28 CB ALA 6 2.036 -7.012 -5.678 1.00 0.00 C ATOM 29 C ALA 6 2.707 -5.774 -7.747 1.00 0.00 C ATOM 30 O ALA 6 3.266 -6.394 -8.653 1.00 0.00 O ATOM 31 N ALA 7 1.783 -4.845 -7.972 1.00 0.00 N ATOM 32 CA ALA 7 1.361 -4.493 -9.322 1.00 0.00 C ATOM 33 CB ALA 7 0.245 -3.447 -9.284 1.00 0.00 C ATOM 34 C ALA 7 2.533 -3.976 -10.149 1.00 0.00 C ATOM 35 O ALA 7 2.658 -4.294 -11.332 1.00 0.00 O ATOM 36 N ALA 8 3.390 -3.178 -9.521 1.00 0.00 N ATOM 37 CA ALA 8 4.552 -2.615 -10.197 1.00 0.00 C ATOM 38 CB ALA 8 5.326 -1.686 -9.260 1.00 0.00 C ATOM 39 C ALA 8 5.472 -3.714 -10.720 1.00 0.00 C ATOM 40 O ALA 8 6.014 -3.613 -11.821 1.00 0.00 O ATOM 41 N ALA 9 5.645 -4.766 -9.923 1.00 0.00 N ATOM 42 CA ALA 9 6.497 -5.884 -10.304 1.00 0.00 C ATOM 43 CB ALA 9 6.565 -6.919 -9.179 1.00 0.00 C ATOM 44 C ALA 9 6.006 -6.541 -11.590 1.00 0.00 C ATOM 45 O ALA 9 6.801 -6.921 -12.448 1.00 0.00 O ATOM 46 N ALA 10 4.688 -6.669 -11.716 1.00 0.00 N ATOM 47 CA ALA 10 4.088 -7.281 -12.896 1.00 0.00 C ATOM 48 CB ALA 10 2.567 -7.360 -12.750 1.00 0.00 C ATOM 49 C ALA 10 4.452 -6.512 -14.162 1.00 0.00 C ATOM 50 O ALA 10 4.723 -7.107 -15.206 1.00 0.00 O ATOM 51 N ALA 11 4.458 -5.187 -14.064 1.00 0.00 N ATOM 52 CA ALA 11 4.789 -4.335 -15.199 1.00 0.00 C ATOM 53 CB ALA 11 4.655 -2.857 -14.824 1.00 0.00 C ATOM 54 C ALA 11 6.198 -4.617 -15.709 1.00 0.00 C ATOM 55 O ALA 11 6.441 -4.639 -16.916 1.00 0.00 O ATOM 56 N ALA 12 7.126 -4.834 -14.781 1.00 0.00 N ATOM 57 CA ALA 12 8.512 -5.115 -15.134 1.00 0.00 C ATOM 58 CB ALA 12 9.371 -5.259 -13.875 1.00 0.00 C ATOM 59 C ALA 12 8.622 -6.375 -15.987 1.00 0.00 C ATOM 60 O ALA 12 9.403 -6.427 -16.937 1.00 0.00 O TER END """ beta_strand_template="""\ ATOM 1 N ALA A 1 -34.967 0.361 0.480 1.00 30.00 N ATOM 2 CA ALA A 1 -33.700 0.830 -0.121 1.00 30.00 C ATOM 3 C ALA A 1 -32.491 0.227 0.567 1.00 30.00 C ATOM 4 O ALA A 1 -32.528 0.205 1.784 1.00 30.00 O ATOM 5 CB ALA A 1 -33.586 2.364 -0.139 1.00 30.00 C ATOM 6 N ALA A 2 -31.529 -0.207 -0.287 1.00 30.00 N ATOM 7 CA ALA A 2 -30.265 -0.830 0.121 1.00 30.00 C ATOM 8 C ALA A 2 -29.092 0.104 -0.268 1.00 30.00 C ATOM 9 O ALA A 2 -29.024 0.723 -1.359 1.00 30.00 O ATOM 10 CB ALA A 2 -29.837 -2.178 -0.470 1.00 30.00 C """ beta_strand_answer="""\ ATOM 1 N ALA A 1 -34.967 0.361 0.480 1.00 30.00 N ATOM 2 CA ALA A 1 -33.700 0.830 -0.121 1.00 30.00 C ATOM 3 C ALA A 1 -32.491 0.227 0.567 1.00 30.00 C ATOM 4 O ALA A 1 -32.528 0.205 1.784 1.00 30.00 O ATOM CB ALA A 1 -33.642 2.352 -0.067 1.00 0.00 C ATOM 1 N ALA A 2 -31.523 -0.190 -0.301 1.00 30.00 N ATOM 2 CA ALA A 2 -30.230 -0.801 0.073 1.00 30.00 C ATOM 3 C ALA A 2 -29.061 0.113 -0.241 1.00 30.00 C ATOM 4 O ALA A 2 -29.096 0.668 -1.324 1.00 30.00 O ATOM CB ALA A 2 -30.071 -2.137 -0.644 1.00 0.00 C ATOM 1 N ALA A 3 -28.126 0.160 0.752 1.00 30.00 N ATOM 2 CA ALA A 3 -26.874 0.947 0.728 1.00 30.00 C ATOM 3 C ALA A 3 -25.649 0.058 0.644 1.00 30.00 C ATOM 4 O ALA A 3 -25.650 -0.919 1.370 1.00 30.00 O ATOM CB ALA A 3 -26.807 1.836 1.964 1.00 0.00 C ATOM 1 N ALA A 4 -24.710 0.510 -0.238 1.00 30.00 N ATOM 2 CA ALA A 4 -23.409 -0.133 -0.523 1.00 30.00 C ATOM 3 C ALA A 4 -22.245 0.697 -0.017 1.00 30.00 C ATOM 4 O ALA A 4 -22.309 1.892 -0.239 1.00 30.00 O ATOM CB ALA A 4 -23.279 -0.379 -2.021 1.00 0.00 C ATOM 1 N ALA A 5 -21.280 -0.042 0.605 1.00 30.00 N ATOM 2 CA ALA A 5 -20.026 0.484 1.186 1.00 30.00 C ATOM 3 C ALA A 5 -18.809 0.032 0.403 1.00 30.00 C ATOM 4 O ALA A 5 -18.794 -1.140 0.074 1.00 30.00 O ATOM CB ALA A 5 -19.917 0.050 2.642 1.00 0.00 C ATOM 1 N ALA A 6 -17.893 1.024 0.201 1.00 30.00 N ATOM 2 CA ALA A 6 -16.605 0.883 -0.511 1.00 30.00 C ATOM 3 C ALA A 6 -15.423 1.013 0.428 1.00 30.00 C ATOM 4 O ALA A 6 -15.486 1.918 1.241 1.00 30.00 O ATOM CB ALA A 6 -16.521 1.921 -1.624 1.00 0.00 C ATOM 1 N ALA A 7 -14.444 0.089 0.202 1.00 30.00 N ATOM 2 CA ALA A 7 -13.170 -0.024 0.945 1.00 30.00 C ATOM 3 C ALA A 7 -11.979 0.343 0.082 1.00 30.00 C ATOM 4 O ALA A 7 -11.980 -0.112 -1.048 1.00 30.00 O ATOM CB ALA A 7 -13.020 -1.440 1.488 1.00 0.00 C ATOM 1 N ALA A 8 -11.064 1.128 0.723 1.00 30.00 N ATOM 2 CA ALA A 8 -9.799 1.631 0.147 1.00 30.00 C ATOM 3 C ALA A 8 -8.588 0.991 0.797 1.00 30.00 C ATOM 4 O ALA A 8 -8.623 0.900 2.011 1.00 30.00 O ATOM CB ALA A 8 -9.741 3.148 0.287 1.00 0.00 C ATOM 1 N ALA A 9 -7.622 0.624 -0.094 1.00 30.00 N ATOM 2 CA ALA A 9 -6.327 -0.006 0.241 1.00 30.00 C ATOM 3 C ALA A 9 -5.160 0.925 -0.022 1.00 30.00 C ATOM 4 O ALA A 9 -5.197 1.540 -1.072 1.00 30.00 O ATOM CB ALA A 9 -6.169 -1.299 -0.550 1.00 0.00 C ATOM 1 N ALA A 10 -4.222 0.916 0.970 1.00 30.00 N ATOM 2 CA ALA A 10 -2.972 1.704 0.988 1.00 30.00 C ATOM 3 C ALA A 10 -1.746 0.822 0.852 1.00 30.00 C ATOM 4 O ALA A 10 -1.745 -0.195 1.522 1.00 30.00 O ATOM CB ALA A 10 -2.902 2.521 2.273 1.00 0.00 C ATOM 1 N ALA A 11 -0.808 1.323 -0.005 1.00 30.00 N ATOM 2 CA ALA A 11 0.492 0.698 -0.328 1.00 30.00 C ATOM 3 C ALA A 11 1.656 1.499 0.222 1.00 30.00 C ATOM 4 O ALA A 11 1.591 2.705 0.068 1.00 30.00 O ATOM CB ALA A 11 0.620 0.538 -1.838 1.00 0.00 C ATOM 1 N ALA A 12 2.623 0.727 0.800 1.00 30.00 N ATOM 2 CA ALA A 12 3.878 1.220 1.406 1.00 30.00 C ATOM 3 C ALA A 12 5.094 0.813 0.597 1.00 30.00 C ATOM 4 O ALA A 12 5.109 -0.338 0.202 1.00 30.00 O ATOM CB ALA A 12 3.990 0.704 2.836 1.00 0.00 C ATOM 1 N ALA A 13 6.009 1.816 0.450 1.00 30.00 N ATOM 2 CA ALA A 13 7.295 1.716 -0.272 1.00 30.00 C ATOM 3 C ALA A 13 8.480 1.793 0.672 1.00 30.00 C ATOM 4 O ALA A 13 8.417 2.651 1.534 1.00 30.00 O ATOM CB ALA A 13 7.377 2.815 -1.324 1.00 0.00 C ATOM 1 N ALA A 14 9.458 0.884 0.392 1.00 30.00 N ATOM 2 CA ALA A 14 10.734 0.730 1.124 1.00 30.00 C ATOM 3 C ALA A 14 11.923 1.146 0.282 1.00 30.00 C ATOM 4 O ALA A 14 11.920 0.756 -0.872 1.00 30.00 O ATOM CB ALA A 14 10.885 -0.714 1.587 1.00 0.00 C ATOM 1 N ALA A 15 12.839 1.894 0.964 1.00 30.00 N ATOM 2 CA ALA A 15 14.103 2.430 0.416 1.00 30.00 C ATOM 3 C ALA A 15 15.315 1.754 1.027 1.00 30.00 C ATOM 4 O ALA A 15 15.283 1.594 2.233 1.00 30.00 O ATOM CB ALA A 15 14.160 3.936 0.642 1.00 0.00 C ATOM 1 N ALA A 16 16.280 1.439 0.114 1.00 30.00 N ATOM 2 CA ALA A 16 17.575 0.791 0.411 1.00 30.00 C ATOM 3 C ALA A 16 18.742 1.737 0.199 1.00 30.00 C ATOM 4 O ALA A 16 18.702 2.410 -0.815 1.00 30.00 O ATOM CB ALA A 16 17.733 -0.454 -0.453 1.00 0.00 C ATOM 1 N ALA A 17 19.681 1.672 1.187 1.00 30.00 N ATOM 2 CA ALA A 17 20.932 2.458 1.247 1.00 30.00 C ATOM 3 C ALA A 17 22.157 1.587 1.058 1.00 30.00 C ATOM 4 O ALA A 17 22.160 0.533 1.670 1.00 30.00 O ATOM CB ALA A 17 21.003 3.201 2.576 1.00 0.00 C ATOM 1 N ALA A 18 23.093 2.136 0.230 1.00 30.00 N ATOM 2 CA ALA A 18 24.393 1.531 -0.131 1.00 30.00 C ATOM 3 C ALA A 18 25.558 2.300 0.462 1.00 30.00 C ATOM 4 O ALA A 18 25.492 3.513 0.377 1.00 30.00 O ATOM CB ALA A 18 24.518 1.457 -1.648 1.00 0.00 C ATOM 1 N ALA A 19 26.526 1.497 0.993 1.00 30.00 N ATOM 2 CA ALA A 19 27.782 1.955 1.625 1.00 30.00 C ATOM 3 C ALA A 19 28.997 1.596 0.792 1.00 30.00 C ATOM 4 O ALA A 19 29.011 0.469 0.331 1.00 30.00 O ATOM CB ALA A 19 27.897 1.359 3.022 1.00 0.00 C ATOM 1 N ALA A 20 29.911 2.606 0.699 1.00 30.00 N ATOM 2 CA ALA A 20 31.196 2.548 -0.029 1.00 30.00 C ATOM 3 C ALA A 20 32.382 2.572 0.915 1.00 30.00 C ATOM 4 O ALA A 20 32.321 3.379 1.825 1.00 30.00 O ATOM CB ALA A 20 31.275 3.705 -1.017 1.00 0.00 C ATOM 1 N ALA A 21 33.361 1.681 0.582 1.00 30.00 N ATOM 2 CA ALA A 21 34.637 1.486 1.303 1.00 30.00 C ATOM 3 C ALA A 21 35.825 1.950 0.482 1.00 30.00 C ATOM 4 O ALA A 21 35.820 1.626 -0.691 1.00 30.00 O ATOM CB ALA A 21 34.791 0.018 1.682 1.00 0.00 C ATOM 1 N ALA A 22 36.741 2.659 1.205 1.00 30.00 N ATOM 2 CA ALA A 22 38.004 3.225 0.685 1.00 30.00 C ATOM 3 C ALA A 22 39.218 2.517 1.254 1.00 30.00 C ATOM 4 O ALA A 22 39.188 2.289 2.450 1.00 30.00 O ATOM CB ALA A 22 38.061 4.716 0.996 1.00 0.00 C TER """ def exercise_00(prefix="exercise_00"): "Build poly-ALA alpha helix" ph = ssb.secondary_structure_from_sequence( alpha_helix_template, "".join(["A"]*12)) ph.atoms().reset_i_seq() #ph.write_pdb_file(file_name="%s_result.pdb"%prefix) sites_1 = ph.atoms().extract_xyz() sites_2 = iotbx.pdb.input(source_info=None, lines=alpha_helix_answer).construct_hierarchy().atoms().extract_xyz() #of = open("1.pdb","w") #print >> of, alpha_helix_answer #of.close() assert sites_1.size()==sites_2.size(), [sites_1.size(),sites_2.size()] d1 = flex.sqrt((sites_1 - sites_2).dot()) rmsd = ssb.calculate_rmsd_smart(ph, iotbx.pdb.input(source_info=None, lines=alpha_helix_answer).construct_hierarchy()) assert rmsd < 0.1, rmsd def exercise_01(prefix="exercise_01"): "Build poly-ALA beta strand" ph = ssb.secondary_structure_from_sequence( beta_strand_template, "".join(["A"]*22)) sites_1 = ph.atoms().extract_xyz() sites_2 = iotbx.pdb.input(source_info=None, lines=beta_strand_answer).construct_hierarchy().atoms().extract_xyz() assert sites_1.size()==sites_2.size() assert approx_equal(sites_1, sites_2, eps=0.002) def exercise_r_t_matrices(): r,t = ssb.get_r_t_matrices_from_structure(alpha_pdb_str) assert approx_equal(r.elems, (-0.02358, 0.96052, 0.27720, -0.86374, -0.15919, 0.47811, 0.50337, -0.22815, 0.83340), eps = 0.0001) assert approx_equal(t.elems, (1.6740, -1.2223, -2.0756), eps = 0.0001) try: ssb.get_r_t_matrices_from_structure(t_pdb_str) except Exception as e: assert str(e) == "pdb_str should contain at least 2 residues" def exercise_secondary_structure_from_sequence(): pdb_inp = iotbx.pdb.input(source_info=None, lines=correct_answer) cs = pdb_inp.xray_structure_simple().crystal_symmetry() correct_h = pdb_inp.construct_hierarchy() test_h = ssb.secondary_structure_from_sequence(alpha_pdb_str, sequence="ACEDGFIHKMLNQPSRTWVY") test_h.atoms().reset_serial() # correct_h.write_pdb_file("correct_h.pdb") # test_h.write_pdb_file("test_h.pdb") # why this passes... for m1, m2 in zip(correct_h.models(), test_h.models()): m1.is_similar_hierarchy( other=m2) m1.is_identical_hierarchy(other=m2) for c1, c2 in zip(m1.chains(), m2.chains()): c1.is_similar_hierarchy( other=c2) c1.is_identical_hierarchy(other=c2) for rg1, rg2 in zip(c1.residue_groups(), c2.residue_groups()): rg1.is_similar_hierarchy( other=rg2) rg1.is_identical_hierarchy(other=rg2) f1 = correct_h.extract_xray_structure(crystal_symmetry=cs).structure_factors( algorithm="direct", d_min=2).f_calc().data() f2 = test_h.extract_xray_structure(crystal_symmetry=cs).structure_factors( algorithm="direct", d_min=2).f_calc().data() assert approx_equal(f1, f2) assert test_h.as_str() == correct_h.as_str() #correct_h.write_pdb_file(file_name="tst_1_ex_last_correct.pdb") #test_h.write_pdb_file(file_name="tst_1_ex_last_out.pdb") # ...and this fails ? # assert correct_h.is_similar_hierarchy(other=test_h) assert approx_equal(test_h.atoms().extract_xyz(), correct_h.atoms().extract_xyz(), eps=0.002) try: ssb.secondary_structure_from_sequence(alpha_pdb_str, sequence="") except Exception as e: assert str(e) == "sequence should contain at least one residue." def exercise(): exercise_00() exercise_01() exercise_r_t_matrices() exercise_secondary_structure_from_sequence() if (__name__ == "__main__"): exercise()